Package Bio :: Package formatdefs :: Module search
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Source Code for Module Bio.formatdefs.search

  1  from Bio.config.FormatRegistry import FormatObject, FormatGroup 
  2   
  3  search = FormatGroup( 
  4      name = "search", 
  5      multirecord = 0, 
  6  ) 
  7   
  8  blast = FormatGroup( 
  9      name = "blast", 
 10      filter = "Bio.expressions.blast.ncbiblast.blast_filter", 
 11      multirecord = 0, 
 12  ) 
 13  search.add(blast) 
 14   
 15  blastp = FormatGroup( 
 16      name = "blastp", 
 17      multirecord = 0, 
 18  ) 
 19  blast.add(blastp) 
 20   
 21  blastn = FormatGroup( 
 22      name = "blastn", 
 23      multirecord = 0, 
 24  ) 
 25  blast.add(blastn) 
 26   
 27  blastx = FormatGroup( 
 28      name = "blastx", 
 29      multirecord = 0, 
 30  ) 
 31  blast.add(blastx) 
 32   
 33  tblastn = FormatGroup( 
 34      name = "tblastn", 
 35      multirecord = 0, 
 36  ) 
 37  blast.add(tblastn) 
 38   
 39  tblastx = FormatGroup( 
 40      name = "tblastx", 
 41      multirecord = 0, 
 42  ) 
 43  blast.add(tblastx) 
 44   
 45  ### NCBI BLASTs 
 46  ncbi_blastp = FormatObject( 
 47      name = "ncbi-blastp", 
 48      abbrev = "ncbi_blastp", 
 49      expression = "Bio.expressions.blast.ncbiblast.blastp", 
 50      filter = "Bio.expressions.blast.ncbiblast.blastp_appheader", 
 51      multirecord = 0, 
 52  ) 
 53  blastp.add(ncbi_blastp) 
 54   
 55  ncbi_blastn = FormatObject( 
 56      name = "ncbi-blastn", 
 57      abbrev = "ncbi_blastn", 
 58      expression = "Bio.expressions.blast.ncbiblast.blastn", 
 59      filter = "Bio.expressions.blast.ncbiblast.blastn_appheader", 
 60      multirecord = 0, 
 61  ) 
 62  blastn.add(ncbi_blastn) 
 63   
 64  ncbi_blastx = FormatObject( 
 65      name = "ncbi-blastx", 
 66      abbrev = "ncbi_blastx", 
 67      expression = "Bio.expressions.blast.ncbiblast.blastx", 
 68      filter = "Bio.expressions.blast.ncbiblast.blastx_appheader", 
 69      multirecord = 0, 
 70  ) 
 71  blastx.add(ncbi_blastx) 
 72   
 73  ncbi_tblastn = FormatObject( 
 74      name = "ncbi-tblastn", 
 75      abbrev = "ncbi_tblastn", 
 76      expression = "Bio.expressions.blast.ncbiblast.tblastn", 
 77      filter = "Bio.expressions.blast.ncbiblast.tblastn_appheader", 
 78      multirecord = 0, 
 79  ) 
 80  tblastn.add(ncbi_tblastn) 
 81   
 82  ncbi_tblastx = FormatObject( 
 83      name = "ncbi-tblastx", 
 84      abbrev = "ncbi_tblastx", 
 85      expression = "Bio.expressions.blast.ncbiblast.tblastx", 
 86      filter = "Bio.expressions.blast.ncbiblast.tblastx_appheader", 
 87      multirecord = 0, 
 88  ) 
 89  tblastx.add(ncbi_tblastx) 
 90   
 91   
 92  ### WU-BLASTs 
 93  wu_blastp = FormatObject( 
 94      name = "wu-blastp", 
 95      abbrev = "wu_blastp", 
 96      expression = "Bio.expressions.blast.wublast.blastp", 
 97      filter = "Bio.expressions.blast.wublast.blastp_appheader", 
 98      multirecord = 0, 
 99  ) 
100  blastp.add(wu_blastp) 
101   
102  wu_blastn = FormatObject( 
103      name = "wu-blastn", 
104      abbrev = "wu_blastn", 
105      expression = "Bio.expressions.blast.wublast.blastn", 
106      filter = "Bio.expressions.blast.wublast.blastn_appheader", 
107      multirecord = 0, 
108  ) 
109  blastn.add(wu_blastn) 
110   
111  wu_blastx = FormatObject( 
112      name = "wu-blastx", 
113      abbrev = "wu_blastx", 
114      expression = "Bio.expressions.blast.wublast.blastx", 
115      filter = "Bio.expressions.blast.wublast.blastx_appheader", 
116      multirecord = 0, 
117  ) 
118  blastx.add(wu_blastx) 
119